# Generated by roxygen2: do not edit by hand

export(addGCBias)

export(annotationMatches)

export(assembleKmers)

export(chromVAR_theme)

export(computeDeviations)

export(computeExpectations)

export(computeVariability)

export(deviationsCovariability)

export(deviationsTsne)

export(differentialDeviations)

export(differentialVariability)

export(filterPeaks)

export(filterSamples)

export(filterSamplesPlot)

export(getAnnotationCorrelation)

export(getAnnotationSynergy)

export(getAnnotations)

export(getBackgroundPeaks)

export(getCisGroups)

export(getCounts)

export(getFragmentsPerPeak)

export(getFragmentsPerSample)

export(getJasparMotifs)

export(getPeaks)

export(getPermutedData)

export(getSampleCorrelation)

export(getSampleDepths)

export(getSampleDistance)

export(getTotalFragments)

export(makeBiasBins)

export(makePermutedSets)

export(matchKmers)

export(plotDeviationsTsne)

export(plotKmerMismatch)

export(plotVariability)

export(pwmDistance)

export(readNarrowpeaks)

exportMethods("annotationMatches<-")

exportMethods('counts<-')

exportMethods(addGCBias)

exportMethods(cbind)

exportMethods(computeDeviations)

exportMethods(computeExpectations)

exportMethods(counts)

exportMethods(deviationScores)

exportMethods(deviations)

exportMethods(getAnnotationCorrelation)

exportMethods(getAnnotationSynergy)

exportMethods(getAnnotations)

exportMethods(getBackgroundPeaks)

exportMethods(getCisGroups)

exportMethods(getFragmentsPerPeak)

exportMethods(getFragmentsPerSample)

exportMethods(getTotalFragments)

exportMethods(makeBiasBins)

exportMethods(makePermutedSets)

exportMethods(matchKmers)

exportMethods(rbind)

import(Biostrings)

import(GenomicRanges)

import(Matrix)

import(SummarizedExperiment)

import(ggplot2)

import(methods)

import(miniUI)

import(shiny)

importClassesFrom(SummarizedExperiment,SummarizedExperiment)

importFrom(BSgenome,getBSgenome)

importFrom(BiocGenerics,relist)

importFrom(BiocParallel,bplapply)

importFrom(Biostrings,nucleotideSubstitutionMatrix)

importFrom(Biostrings,stringDist)

importFrom(DT,datatable)

importFrom(DT,formatSignif)

importFrom(GenomeInfoDb,"seqlevels<-")

importFrom(GenomeInfoDb,seqlevels)

importFrom(GenomeInfoDb,seqnames)

importFrom(GenomeInfoDb,sortSeqlevels)

importFrom(IRanges,IRanges)

importFrom(IRanges,PartitioningByEnd)

importFrom(IRanges,overlapsAny)

importFrom(Rcpp,sourceCpp)

importFrom(Rsamtools,ScanBamParam)

importFrom(Rsamtools,countBam)

importFrom(Rsamtools,scanBam)

importFrom(Rsamtools,scanBamFlag)

importFrom(S4Vectors,DataFrame)

importFrom(S4Vectors,elementNROWS)

importFrom(S4Vectors,isSorted)

importFrom(S4Vectors,queryHits)

importFrom(S4Vectors,subjectHits)

importFrom(TFBSTools,PWMatrix)

importFrom(TFBSTools,PWMatrixList)

importFrom(TFBSTools,bg)

importFrom(TFBSTools,name)

importFrom(graphics,text)

importFrom(plotly,ggplotly)

importFrom(plotly,plotlyOutput)

importFrom(plotly,renderPlotly)

importFrom(stats,aggregate)

importFrom(stats,anova)

importFrom(stats,approx)

importFrom(stats,as.dist)

importFrom(stats,cor)

importFrom(stats,cov)

importFrom(stats,dist)

importFrom(stats,dnorm)

importFrom(stats,hclust)

importFrom(stats,kruskal.test)

importFrom(stats,lm)

importFrom(stats,median)

importFrom(stats,na.omit)

importFrom(stats,oneway.test)

importFrom(stats,p.adjust)

importFrom(stats,pchisq)

importFrom(stats,pnorm)

importFrom(stats,prcomp)

importFrom(stats,quantile)

importFrom(stats,runif)

importFrom(stats,sd)

importFrom(stats,t.test)

importFrom(stats,var)

importFrom(stats,wilcox.test)

importFrom(utils,installed.packages)

importFrom(utils,read.delim)

importFrom(utils,setTxtProgressBar)

importFrom(utils,txtProgressBar)

importMethodsFrom(BiocGenerics,"counts<-")

importMethodsFrom(BiocGenerics,counts)

importMethodsFrom(GenomicRanges,end)

importMethodsFrom(GenomicRanges,sort)

importMethodsFrom(GenomicRanges,start)

useDynLib(chromVAR, .registration = TRUE)